@jafreck/lore 0.3.7 → 0.3.8

package/dist/indexer/index.js

@@ -7,20 +7,24 @@
  * For full builds, `build()` delegates entirely to the pipeline which
  * enforces the data-dependency chain:
  * ```
- * SourceIndexStage → DocsIndexStage → ImportResolutionStage
- *   → DependencyApiStage → ScipEnrichmentStage → LspEnrichmentStage
- *   → ResolutionStage → TestMapStage → HistoryStage → EmbeddingStage
+ * ScipIndexerStage → SourceIndexStage → DocsIndexStage
+ *   → ImportResolutionStage → DependencyApiStage
+ *   → LspEnrichmentStage → ResolutionStage → TestMapStage
+ *   → HistoryStage → EmbeddingStage
  * ```
  *
- * For incremental updates, `update()` uses stage-extracted helpers
- * while managing the changed-file diff itself.
+ * `ScipIndexerStage` now populates both structural data (symbols, refs)
+ * and enrichment metadata (type signatures, definition locations) in a
+ * single pass.  `SourceIndexStage` then adds tree-sitter metrics
+ * (complexity, nesting depth) to SCIP-sourced files and handles
+ * remaining languages.
  *
  * The enrichment → resolution ordering is **load-bearing** and enforced
  * structurally by the pipeline rather than by call-site discipline.
  */
 import * as fs from 'node:fs';
 import { execFileSync } from 'node:child_process';
-import { openDb, setLoreMeta, LORE_META_LAST_HEAD_SHA, LORE_META_COVERAGE_LAST_SOURCE_PATH, LORE_META_COVERAGE_LAST_SOURCE_MTIME, } from '../db/schema.js';
+import { openDb, setLoreMeta, incrementGeneration, LORE_META_LAST_HEAD_SHA, LORE_META_GENERATION_PENDING, LORE_META_COVERAGE_LAST_SOURCE_PATH, LORE_META_COVERAGE_LAST_SOURCE_MTIME, } from '../db/schema.js';
 import { DEFAULT_EMBEDDING_MODEL } from '../embeddings/embedder.js';
 import { ingestCoverageReport } from '../testing/coverage.js';
 import { resolveSymbolEdges } from '../resolution/call-graph.js';
@@ -28,7 +32,7 @@ import { refreshTestMappings } from '../testing/test-mapper.js';
 import { ingestGitHistory } from '../git/history.js';
 import { getLogger } from '../logger.js';
 import { IndexPipeline } from './pipeline.js';
-import { ScipSourceStage, SourceIndexStage, DocsIndexStage, ImportResolutionStage, DependencyApiStage, ScipEnrichmentStage, LspEnrichmentStage, EmbeddingStage, } from './stages/index.js';
+import { ScipIndexerStage, SourceIndexStage, DocsIndexStage, ImportResolutionStage, DependencyApiStage, LspEnrichmentStage, EmbeddingStage, ReverseDepsStage, OverlayCleanupStage, } from './stages/index.js';
 // ─── IndexBuilder (façade) ────────────────────────────────────────────────────
 /**
  * Façade over the composable `IndexPipeline`.
@@ -49,7 +53,6 @@ export class IndexBuilder {
     history;
     indexDependencies;
     embeddingModel;
-    docsAutoNotes;
     lspSettings;
     scipSettings;
     constructor(dbPath, walkerConfig, embedder, embeddingModelOrOptions) {
@@ -67,7 +70,6 @@ export class IndexBuilder {
             this.embedder = null;
         }
         this.history = opts.history ?? false;
-        this.docsAutoNotes = opts.docsAutoNotes ?? true;
         this.indexDependencies = opts.indexDependencies ?? false;
         this.lspSettings = opts.lsp ?? null;
         this.scipSettings = opts.scip ?? null;
@@ -86,25 +88,29 @@ export class IndexBuilder {
         const branch = this.resolveBranch();
         log.indexing('build started', { dbPath: this.dbPath, branch, rootDir: this.walkerConfig.rootDir });
         // Build the pipeline with all stages in dependency order.
-        // ScipSourceStage runs first for SCIP-covered languages (symbols + refs
-        // from SCIP directly).  SourceIndexStage then handles remaining languages
-        // via tree-sitter.  LSP enrichment is optional for both paths.
+        // ScipIndexerStage runs first for SCIP-covered languages (symbols + refs
+        // from SCIP directly, with enrichment metadata populated inline).
+        // SourceIndexStage then adds tree-sitter metrics to SCIP files and
+        // handles remaining languages.  LSP enrichment is optional.
         //
         // Stages in arrays run concurrently:
         //   - SourceIndexStage + DocsIndexStage: write to disjoint tables.
-        //   - HistoryStage + ScipEnrichment + LspEnrichment: history writes to
+        //   - HistoryStage + LspEnrichment: history writes to
         //     commits/commit_files (disjoint from enrichment targets).
         const pipeline = new IndexPipeline([
-            new ScipSourceStage(),
+            new ScipIndexerStage(),
             [new SourceIndexStage(), new DocsIndexStage()],
             new ImportResolutionStage(),
             new DependencyApiStage(),
-            [new ScipEnrichmentStage(), new LspEnrichmentStage(), historyStage()],
+            [new LspEnrichmentStage(), historyStage()],
             ftsRefreshStage(),
             resolutionStage(),
             testMapStage(),
+            new ReverseDepsStage(),
             new EmbeddingStage(),
         ]);
+        // Baseline: set generation to 1 for initial build.
+        const generation = incrementGeneration(db);
         const context = {
             db,
             dbPath: this.dbPath,
@@ -117,11 +123,12 @@ export class IndexBuilder {
             files: [],
             indexDependencies: this.indexDependencies,
             history: this.history,
-            docsAutoNotes: this.docsAutoNotes,
             staleSymbolIds: [],
             changedSourcePaths: [],
             changedDocPaths: [],
             sourceCache: new Map(),
+            layer: 'baseline',
+            generation,
         };
         try {
             await pipeline.run(context, 'build');
@@ -144,10 +151,10 @@ export class IndexBuilder {
         }
     }
     /**
-     * Incrementally re-processes only the listed files and updates the DB.
+     * Incrementally re-processes only the listed files using the overlay layer.
      *
-     * Delegates to the same pipeline as `build()` — each stage handles
-     * `'update'` mode by operating only on the changed-file set.
+     * Tree-sitter is the primary indexer; LSP enriches cross-file refs.
+     * SCIP is never invoked during overlay updates.
      *
      * @param changedFiles  Absolute paths of files that have changed.
      */
@@ -155,15 +162,18 @@ export class IndexBuilder {
         const db = openDb(this.dbPath);
         const branch = this.resolveBranch();
         const log = getLogger();
+        // Overlay pipeline: tree-sitter → imports → LSP → resolution → reverse-deps → embedding
+        // No SCIP stage — tree-sitter is the primary incremental indexer.
         const pipeline = new IndexPipeline([
-            new ScipSourceStage(),
+            new ScipIndexerStage(),
             [new SourceIndexStage(), new DocsIndexStage()],
             new ImportResolutionStage(),
             new DependencyApiStage(),
-            [new ScipEnrichmentStage(), new LspEnrichmentStage(), historyStage()],
+            [new LspEnrichmentStage(), historyStage()],
             ftsRefreshStage(),
             resolutionStage(),
             testMapStage(),
+            new ReverseDepsStage(),
             new EmbeddingStage(),
         ]);
         const context = {
@@ -178,12 +188,13 @@ export class IndexBuilder {
             files: [],
             indexDependencies: this.indexDependencies,
             history: this.history,
-            docsAutoNotes: this.docsAutoNotes,
             changedFiles,
             staleSymbolIds: [],
             changedSourcePaths: [],
             changedDocPaths: [],
             sourceCache: new Map(),
+            layer: 'overlay',
+            generation: 0,
         };
         try {
             await pipeline.run(context, 'update');
@@ -193,6 +204,67 @@ export class IndexBuilder {
             db.close();
         }
     }
+    /**
+     * Perform a background baseline rebuild (SCIP reconciliation).
+     *
+     * Writes to a new generation, then atomically promotes and cleans
+     * stale overlay rows.  This is the only path that invokes SCIP.
+     */
+    async baselineRebuild() {
+        const log = getLogger();
+        const rebuildStart = performance.now();
+        const rebuildStartedAt = Math.floor(Date.now() / 1000);
+        const db = openDb(this.dbPath);
+        const branch = this.resolveBranch();
+        // Increment pending generation
+        const newGeneration = incrementGeneration(db);
+        setLoreMeta(db, LORE_META_GENERATION_PENDING, String(newGeneration));
+        log.indexing('baseline rebuild started', { generation: newGeneration });
+        const pipeline = new IndexPipeline([
+            new ScipIndexerStage(),
+            [new SourceIndexStage(), new DocsIndexStage()],
+            new ImportResolutionStage(),
+            new DependencyApiStage(),
+            [new LspEnrichmentStage(), historyStage()],
+            ftsRefreshStage(),
+            resolutionStage(),
+            testMapStage(),
+            new EmbeddingStage(),
+            new OverlayCleanupStage({
+                newGeneration,
+                rebuildStartedAt,
+                headSha: this.readGitValue(['rev-parse', 'HEAD']),
+            }),
+        ]);
+        const context = {
+            db,
+            dbPath: this.dbPath,
+            walkerConfig: this.walkerConfig,
+            branch,
+            lsp: this.lspSettings,
+            scip: this.scipSettings,
+            embedder: this.embedder,
+            log,
+            files: [],
+            indexDependencies: this.indexDependencies,
+            history: this.history,
+            staleSymbolIds: [],
+            changedSourcePaths: [],
+            changedDocPaths: [],
+            sourceCache: new Map(),
+            layer: 'baseline',
+            generation: newGeneration,
+        };
+        try {
+            await pipeline.run(context, 'build');
+            this.saveLastKnownHead(db);
+            const indexDurationMs = Math.round(performance.now() - rebuildStart);
+            log.indexing('baseline rebuild complete', { generation: newGeneration, durationMs: indexDurationMs });
+        }
+        finally {
+            db.close();
+        }
+    }
     /**
      * Writes an LLM-generated summary for a symbol to `symbol_summaries`.
      */
@@ -279,7 +351,9 @@ export class IndexBuilder {
 function resolutionStage() {
     return {
         name: 'symbol-resolution',
-        execute: async (ctx) => { resolveSymbolEdges(ctx.db); },
+        execute: async (ctx) => {
+            resolveSymbolEdges(ctx.db, { overlayOnly: ctx.layer === 'overlay' });
+        },
     };
 }
 /** Refresh test-to-source file mappings. */
@@ -301,6 +375,7 @@ function ftsRefreshStage() {
         execute: async (ctx) => {
             ctx.db.transaction(() => {
                 ctx.db.exec('DELETE FROM symbols_fts');
+                // Use effective_symbols view to index only the active layer's symbols
                 ctx.db.exec(`
           INSERT INTO symbols_fts(rowid, name, signature, kind)
           SELECT s.id,
@@ -310,7 +385,7 @@ function ftsRefreshStage() {
                  COALESCE(s.signature, '')                || char(10) ||
                  s.name,
                  s.kind
-          FROM symbols s
+          FROM effective_symbols s
         `);
             })();
         },

package/dist/indexer/index.js.map

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package/dist/indexer/pipeline.d.ts

@@ -7,18 +7,19 @@
  * ## Stage ordering (data-dependency chain)
  *
  * ```
- * ScipSourceStage → SourceIndexStage → DocsIndexStage
+ * ScipIndexerStage → SourceIndexStage → DocsIndexStage
  *   → ImportResolutionStage → DependencyApiStage
  *   → LspEnrichmentStage → ResolutionStage
  *   → TestMapStage → HistoryStage → EmbeddingStage
  * ```
  *
- * `ScipSourceStage` runs first for SCIP-covered languages, populating
- * symbols AND refs directly with pre-resolved edges.  `SourceIndexStage`
- * then handles remaining languages via tree-sitter.
+ * `ScipIndexerStage` runs first for SCIP-covered languages, populating
+ * symbols AND refs directly with pre-resolved edges and enrichment
+ * metadata (type signatures, definition locations) in a single pass.
+ * `SourceIndexStage` then adds tree-sitter metrics (complexity, nesting)
+ * to SCIP-sourced files and handles remaining languages.
  *
- * LSP enrichment is optional for both paths (adds type signatures to
- * SCIP-sourced symbols, enriches non-SCIP refs with definition data).
+ * LSP enrichment is optional (enriches non-SCIP refs with definition data).
  *
  * The resolution stage only processes refs that are still `unresolved`
  * (i.e. non-SCIP languages without LSP enrichment).
@@ -67,8 +68,6 @@ export interface PipelineContext {
         depth?: number;
         all?: boolean;
     };
-    /** Whether to auto-seed documentation notes. */
-    docsAutoNotes: boolean;
     /**
      * Absolute paths of changed files supplied by the caller for incremental
      * updates.  Undefined in build mode.
@@ -91,28 +90,40 @@ export interface PipelineContext {
     changedDocPaths: string[];
     /**
      * Languages for which SCIP enrichment already provided data.
-     * Set by `ScipEnrichmentStage`; read by `LspEnrichmentStage` to skip
+     * Set by `ScipIndexerStage`; read by `LspEnrichmentStage` to skip
      * languages that don't need LSP fallback.
      */
     scipCoveredLanguages?: ReadonlySet<string>;
     /**
      * Languages fully sourced from SCIP (symbols + refs).
-     * Set by `ScipSourceStage`; read by `SourceIndexStage` to skip
+     * Set by `ScipIndexerStage`; read by `SourceIndexStage` to skip
      * tree-sitter extraction for these languages, and by `LspEnrichmentStage`.
      */
     scipSourcedLanguages?: ReadonlySet<string>;
     /**
      * Absolute file paths sourced from SCIP.
-     * Set by `ScipSourceStage`; read by `SourceIndexStage` to skip files.
+     * Set by `ScipIndexerStage`; read by `SourceIndexStage` to skip files.
      */
     scipSourcedFiles?: ReadonlySet<string>;
     /**
      * In-memory cache of source file contents (path → source text).
-     * Populated by SourceIndexStage / ScipSourceStage during parsing.
-     * Later stages (SCIP enrichment, LSP enrichment) read from here to
+     * Populated by SourceIndexStage / ScipIndexerStage during parsing.
+     * Later stages (LSP enrichment) read from here to
      * avoid redundant `readFileSync` calls.
      */
     sourceCache: Map<string, string>;
+    /**
+     * The layer that stages should write to:
+     *  - `'baseline'` for full SCIP builds.
+     *  - `'overlay'` for tree-sitter + LSP incremental updates.
+     */
+    layer: 'baseline' | 'overlay';
+    /**
+     * Baseline generation counter produced by SCIP.
+     * Baseline rows are written with this value.
+     * Overlay rows always use `generation = 0`.
+     */
+    generation: number;
 }
 /**
  * A composable pipeline stage.
@@ -153,7 +164,7 @@ export type PipelineEntry = PipelineStage | PipelineStage[];
  * @example
  * ```ts
  * const pipeline = new IndexPipeline([
- *   new ScipSourceStage(),
+ *   new ScipIndexerStage(),
  *   [new SourceIndexStage(), new DocsIndexStage()],  // run in parallel
  *   new ImportResolutionStage(),
  *   new EmbeddingStage(),

package/dist/indexer/pipeline.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"pipeline.d.ts","sourceRoot":"","sources":["../../src/indexer/pipeline.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;GAyBG;AAEH,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,wBAAwB,CAAC;AAC3D,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,2BAA2B,CAAC;AACnE,OAAO,KAAK,EAAE,oBAAoB,EAAE,MAAM,kBAAkB,CAAC;AAC7D,OAAO,KAAK,EAAE,qBAAqB,EAAE,MAAM,mBAAmB,CAAC;AAC/D,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,cAAc,CAAC;AAK/C;;;GAGG;AACH,MAAM,WAAW,eAAe;IAC9B,kCAAkC;IAClC,EAAE,EAAE,QAAQ,CAAC,QAAQ,CAAC;IACtB,4EAA4E;IAC5E,MAAM,EAAE,MAAM,CAAC;IACf,oDAAoD;IACpD,YAAY,EAAE,YAAY,CAAC;IAC3B,4BAA4B;IAC5B,MAAM,EAAE,MAAM,CAAC;IACf,gDAAgD;IAChD,GAAG,EAAE,oBAAoB,GAAG,IAAI,CAAC;IACjC,iDAAiD;IACjD,IAAI,EAAE,qBAAqB,GAAG,IAAI,CAAC;IACnC,mCAAmC;IACnC,QAAQ,EAAE,iBAAiB,GAAG,IAAI,CAAC;IACnC,uBAAuB;IACvB,GAAG,EAAE,UAAU,CAAC;IAEhB;;;;;OAKG;IACH,KAAK,EAAE,KAAK,CAAC;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,QAAQ,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IAEjD,8DAA8D;IAC9D,iBAAiB,EAAE,OAAO,CAAC;IAC3B,gCAAgC;IAChC,OAAO,EAAE,OAAO,GAAG;QAAE,KAAK,CAAC,EAAE,MAAM,CAAC;QAAC,GAAG,CAAC,EAAE,OAAO,CAAA;KAAE,CAAC;IAIrD;;;OAGG;IACH,YAAY,CAAC,EAAE,MAAM,EAAE,CAAC;IAExB;;;OAGG;IACH,cAAc,EAAE,MAAM,EAAE,CAAC;IAEzB;;;OAGG;IACH,kBAAkB,EAAE,MAAM,EAAE,CAAC;IAE7B;;;OAGG;IACH,eAAe,EAAE,MAAM,EAAE,CAAC;IAE1B;;;;OAIG;IACH,oBAAoB,CAAC,EAAE,WAAW,CAAC,MAAM,CAAC,CAAC;IAE3C;;;;OAIG;IACH,oBAAoB,CAAC,EAAE,WAAW,CAAC,MAAM,CAAC,CAAC;IAE3C;;;OAGG;IACH,gBAAgB,CAAC,EAAE,WAAW,CAAC,MAAM,CAAC,CAAC;IAEvC;;;;;OAKG;IACH,WAAW,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAIjC;;;;OAIG;IACH,KAAK,EAAE,UAAU,GAAG,SAAS,CAAC;IAE9B;;;;OAIG;IACH,UAAU,EAAE,MAAM,CAAC;CACpB;AAED;;;;;GAKG;AACH,MAAM,WAAW,aAAa;IAC5B,mDAAmD;IACnD,QAAQ,CAAC,IAAI,EAAE,MAAM,CAAC;IAEtB;;;;;OAKG;IACH,OAAO,CAAC,OAAO,EAAE,eAAe,EAAE,IAAI,EAAE,OAAO,GAAG,QAAQ,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;IAE3E;;;OAGG;IACH,OAAO,CAAC,IAAI,OAAO,CAAC,IAAI,CAAC,CAAC;CAC3B;AAID;;;;GAIG;AACH,MAAM,MAAM,aAAa,GAAG,aAAa,GAAG,aAAa,EAAE,CAAC;AAI5D;;;;;;;;;;;;;;;;;;GAkBG;AACH,qBAAa,aAAa;IACxB,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAkB;gBAE9B,OAAO,EAAE,aAAa,EAAE;IAIpC;;;OAGG;IACG,GAAG,CAAC,OAAO,EAAE,eAAe,EAAE,IAAI,EAAE,OAAO,GAAG,QAAQ,GAAG,OAAO,CAAC,IAAI,CAAC;IAuD5E,kFAAkF;IAClF,IAAI,UAAU,IAAI,MAAM,EAAE,CAEzB;CACF"}

package/dist/indexer/pipeline.js

@@ -7,18 +7,19 @@
  * ## Stage ordering (data-dependency chain)
  *
  * ```
- * ScipSourceStage → SourceIndexStage → DocsIndexStage
+ * ScipIndexerStage → SourceIndexStage → DocsIndexStage
  *   → ImportResolutionStage → DependencyApiStage
  *   → LspEnrichmentStage → ResolutionStage
  *   → TestMapStage → HistoryStage → EmbeddingStage
  * ```
  *
- * `ScipSourceStage` runs first for SCIP-covered languages, populating
- * symbols AND refs directly with pre-resolved edges.  `SourceIndexStage`
- * then handles remaining languages via tree-sitter.
+ * `ScipIndexerStage` runs first for SCIP-covered languages, populating
+ * symbols AND refs directly with pre-resolved edges and enrichment
+ * metadata (type signatures, definition locations) in a single pass.
+ * `SourceIndexStage` then adds tree-sitter metrics (complexity, nesting)
+ * to SCIP-sourced files and handles remaining languages.
  *
- * LSP enrichment is optional for both paths (adds type signatures to
- * SCIP-sourced symbols, enriches non-SCIP refs with definition data).
+ * LSP enrichment is optional (enriches non-SCIP refs with definition data).
  *
  * The resolution stage only processes refs that are still `unresolved`
  * (i.e. non-SCIP languages without LSP enrichment).
@@ -36,7 +37,7 @@ import { getLogger } from '../logger.js';
  * @example
  * ```ts
  * const pipeline = new IndexPipeline([
- *   new ScipSourceStage(),
+ *   new ScipIndexerStage(),
  *   [new SourceIndexStage(), new DocsIndexStage()],  // run in parallel
  *   new ImportResolutionStage(),
  *   new EmbeddingStage(),

package/dist/indexer/pipeline.js.map

@@ -1 +1 @@
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package/dist/indexer/stages/docs-index.d.ts

@@ -2,19 +2,17 @@
  * @module indexer/stages/docs-index
  *
  * Pipeline stage: walk documentation files, chunk by headings, insert into
- * the database, and optionally seed notes from documentation content.
+ * the database.
  */
 import type { PipelineContext, PipelineStage } from '../pipeline.js';
 import type { Database } from '../../db/schema.js';
 import type { DocumentationFile } from '../../docs/docs.js';
 /**
  * Walk documentation files, chunk by headings, and persist to the database.
- * Optionally seeds notes from documentation content.
  */
 export declare class DocsIndexStage implements PipelineStage {
     readonly name = "docs-index";
     execute(context: PipelineContext, mode: 'build' | 'update'): Promise<void>;
 }
 export declare function processDocumentationFile(db: Database.Database, doc: DocumentationFile, branch: string): void;
-export declare function upsertSeededDocumentationNote(db: Database.Database, doc: DocumentationFile, branch: string): void;
 //# sourceMappingURL=docs-index.d.ts.map

package/dist/indexer/stages/docs-index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"docs-index.d.ts","sourceRoot":"","sources":["../../../src/indexer/stages/docs-index.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAGH,OAAO,KAAK,EAAE,eAAe,EAAE,aAAa,EAAE,MAAM,gBAAgB,CAAC;AACrE,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,oBAAoB,CAAC;AAEnD,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAC;AAiB5D;;;GAGG;AACH,qBAAa,cAAe,YAAW,aAAa;IAClD,QAAQ,CAAC,IAAI,gBAAgB;IAEvB,OAAO,CAAC,OAAO,EAAE,eAAe,EAAE,IAAI,EAAE,OAAO,GAAG,QAAQ,GAAG,OAAO,CAAC,IAAI,CAAC;CAsCjF;AAID,wBAAgB,wBAAwB,CACtC,EAAE,EAAE,QAAQ,CAAC,QAAQ,EACrB,GAAG,EAAE,iBAAiB,EACtB,MAAM,EAAE,MAAM,GACb,IAAI,CAsEN;AAED,wBAAgB,6BAA6B,CAC3C,EAAE,EAAE,QAAQ,CAAC,QAAQ,EACrB,GAAG,EAAE,iBAAiB,EACtB,MAAM,EAAE,MAAM,GACb,IAAI,CAsBN"}
+{"version":3,"file":"docs-index.d.ts","sourceRoot":"","sources":["../../../src/indexer/stages/docs-index.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAGH,OAAO,KAAK,EAAE,eAAe,EAAE,aAAa,EAAE,MAAM,gBAAgB,CAAC;AACrE,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,oBAAoB,CAAC;AAEnD,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAC;AAW5D;;GAEG;AACH,qBAAa,cAAe,YAAW,aAAa;IAClD,QAAQ,CAAC,IAAI,gBAAgB;IAEvB,OAAO,CAAC,OAAO,EAAE,eAAe,EAAE,IAAI,EAAE,OAAO,GAAG,QAAQ,GAAG,OAAO,CAAC,IAAI,CAAC;CAkCjF;AAID,wBAAgB,wBAAwB,CACtC,EAAE,EAAE,QAAQ,CAAC,QAAQ,EACrB,GAAG,EAAE,iBAAiB,EACtB,MAAM,EAAE,MAAM,GACb,IAAI,CAsEN"}

package/dist/indexer/stages/docs-index.js

@@ -2,14 +2,12 @@
  * @module indexer/stages/docs-index
  *
  * Pipeline stage: walk documentation files, chunk by headings, insert into
- * the database, and optionally seed notes from documentation content.
+ * the database.
  */
 import { walkDocumentationFiles } from '../../discovery/walker.js';
-import { inferSeededDocNoteKey, buildDocNoteScope } from '../../docs/docs.js';
 // ─── Stage ────────────────────────────────────────────────────────────────────
 /**
  * Walk documentation files, chunk by headings, and persist to the database.
- * Optionally seeds notes from documentation content.
  */
 export class DocsIndexStage {
     name = 'docs-index';
@@ -23,9 +21,6 @@ export class DocsIndexStage {
                 for (const doc of docs) {
                     seenDocPaths.add(doc.path);
                     processDocumentationFile(db, doc, branch);
-                    if (context.docsAutoNotes) {
-                        upsertSeededDocumentationNote(db, doc, branch);
-                    }
                 }
                 removeStaleDocumentation(db, branch, seenDocPaths);
             })();
@@ -40,8 +35,6 @@ export class DocsIndexStage {
                     const changedDoc = docsByPath.get(filePath);
                     if (changedDoc) {
                         processDocumentationFile(db, changedDoc, branch);
-                        if (context.docsAutoNotes)
-                            upsertSeededDocumentationNote(db, changedDoc, branch);
                         context.changedDocPaths.push(filePath);
                     }
                     else {
@@ -96,23 +89,6 @@ export function processDocumentationFile(db, doc, branch) {
        WHERE id IN (${staleSectionIds.map(() => '?').join(', ')})`).run(...staleSectionIds);
     }
 }
-export function upsertSeededDocumentationNote(db, doc, branch) {
-    const key = inferSeededDocNoteKey(doc);
-    if (!key)
-        return;
-    const scope = buildDocNoteScope(doc.path, branch);
-    const existing = db.prepare('SELECT content, source_hash FROM notes WHERE key = ? AND scope = ?').get(key, scope);
-    if (existing?.content === doc.content && existing.source_hash === doc.hash) {
-        return;
-    }
-    db.prepare(`INSERT INTO notes (key, scope, content, model, source_hash, created_at, updated_at)
-     VALUES (?, ?, ?, ?, ?, unixepoch(), unixepoch())
-     ON CONFLICT(key, scope) DO UPDATE SET
-       content = excluded.content,
-       model = excluded.model,
-       source_hash = excluded.source_hash,
-       updated_at = unixepoch()`).run(key, scope, doc.content, 'system:auto-doc-seed', doc.hash);
-}
 function deleteDocumentationByPath(db, docPath, branch) {
     const row = db.prepare('SELECT id FROM docs WHERE path = ? AND branch = ?')
         .get(docPath, branch);

package/dist/indexer/stages/docs-index.js.map

@@ -1 +1 @@
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package/dist/indexer/stages/index.d.ts

@@ -3,12 +3,14 @@
  *
  * Concrete pipeline stages with real implementations.
  */
-export { ScipSourceStage } from './scip-source.js';
+export { ScipIndexerStage } from './scip-indexer.js';
 export { SourceIndexStage } from './source-index.js';
 export { DocsIndexStage } from './docs-index.js';
 export { ImportResolutionStage } from './import-resolution.js';
 export { DependencyApiStage } from './dependency-api.js';
-export { ScipEnrichmentStage } from './scip-enrichment.js';
 export { LspEnrichmentStage } from './lsp-enrichment.js';
 export { EmbeddingStage } from './embedding.js';
+export { ReverseDepsStage } from './reverse-deps.js';
+export { OverlayCleanupStage } from './overlay-cleanup.js';
+export type { OverlayCleanupOptions } from './overlay-cleanup.js';
 //# sourceMappingURL=index.d.ts.map

package/dist/indexer/stages/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/indexer/stages/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAC;AACnD,OAAO,EAAE,gBAAgB,EAAE,MAAM,mBAAmB,CAAC;AACrD,OAAO,EAAE,cAAc,EAAE,MAAM,iBAAiB,CAAC;AACjD,OAAO,EAAE,qBAAqB,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,kBAAkB,EAAE,MAAM,qBAAqB,CAAC;AACzD,OAAO,EAAE,mBAAmB,EAAE,MAAM,sBAAsB,CAAC;AAC3D,OAAO,EAAE,kBAAkB,EAAE,MAAM,qBAAqB,CAAC;AACzD,OAAO,EAAE,cAAc,EAAE,MAAM,gBAAgB,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/indexer/stages/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,mBAAmB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,mBAAmB,CAAC;AACrD,OAAO,EAAE,cAAc,EAAE,MAAM,iBAAiB,CAAC;AACjD,OAAO,EAAE,qBAAqB,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,kBAAkB,EAAE,MAAM,qBAAqB,CAAC;AACzD,OAAO,EAAE,kBAAkB,EAAE,MAAM,qBAAqB,CAAC;AACzD,OAAO,EAAE,cAAc,EAAE,MAAM,gBAAgB,CAAC;AAChD,OAAO,EAAE,gBAAgB,EAAE,MAAM,mBAAmB,CAAC;AACrD,OAAO,EAAE,mBAAmB,EAAE,MAAM,sBAAsB,CAAC;AAC3D,YAAY,EAAE,qBAAqB,EAAE,MAAM,sBAAsB,CAAC"}

package/dist/indexer/stages/index.js

@@ -3,12 +3,13 @@
  *
  * Concrete pipeline stages with real implementations.
  */
-export { ScipSourceStage } from './scip-source.js';
+export { ScipIndexerStage } from './scip-indexer.js';
 export { SourceIndexStage } from './source-index.js';
 export { DocsIndexStage } from './docs-index.js';
 export { ImportResolutionStage } from './import-resolution.js';
 export { DependencyApiStage } from './dependency-api.js';
-export { ScipEnrichmentStage } from './scip-enrichment.js';
 export { LspEnrichmentStage } from './lsp-enrichment.js';
 export { EmbeddingStage } from './embedding.js';
+export { ReverseDepsStage } from './reverse-deps.js';
+export { OverlayCleanupStage } from './overlay-cleanup.js';
 //# sourceMappingURL=index.js.map

package/dist/indexer/stages/index.js.map

@@ -1 +1 @@
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